DNA Origami Technology Research Articles

Mechanically Interlocked DNA nanostructures for Functional Devices

CONSPECTUS: Self-assembled functional DNA oligonucleotide based architectures represent highly promising candidates for the creation of nanoscale devices. The field of DNA nanotechnology has emerged to a high level of maturity and currently constitutes one of the most dynamic, creative, and exciting modern research areas. The transformation from structural DNA nanotechnology to functional DNA architectures is already taking place with tremendous pace. Particularly the advent of DNA origami technology has propelled DNA nanotechnology forward. DNA origami provided a versatile method for precisely aligning structural and functional DNA modules in two and three dimensions, thereby serving as a means for constructing scaffolds and chassis required for the precise orchestration of multiple functional DNA architectures. Key modules of these will contain interlocked nanomechanical components made of DNA. The mechanical interlocking allows for performing highly specific and controlled motion, by reducing the dimensionality of diffusion-controlled processes without restrictions in motional flexibility. Examples for nanoscale interlocked DNA architectures illustrate how elementary functional units of future nanomachines can be designed and realized, and show what role interlocked DNA architectures may play in this endeavor. Functional supramolecular systems, in general, and nanomachinery, in particular, self-organize into architectures that reflect different levels of complexity with respect to their function, their arrangement in the second and third dimension, their suitability for different purposes, and their functional interplay. Toward this goal, DNA nanotechnology and especially the DNA origami technology provide opportunities for nanomechanics, nanorobotics, and nanomachines. In this Account, we address approaches that apply to the construction of interlocked DNA nanostructures, drawing largely form our own contributions to interlocked architectures based on double-stranded (ds) circular geometries, and describe progress, opportunities, and challenges in rotaxanes and pseudorotaxanes made of dsDNA. Operating nanomechanical devices in a reliable and repetitive fashion requires methods for switching movable parts in DNA nanostructures from one state to another. An important issue is the orthogonality of switches that allow for operating different parts in parallel under spatiotemporal control. A variety of switching methods have been applied to switch individual components in interlocked DNA nanostructures like rotaxanes and catenanes. They are based on toehold, light, pseudocomplementary peptide nucleic acids (pcPNAs), and others. The key issues discussed here illustrate our perspective on the future prospects of interlocked DNA-based devices and the challenges that lay ahead.

Synthetic Membrane Curvature-Inducing DNA Origami Scaffolds

Biological membranes are dynamic cellular barriers that suffer deformation and bending. Despite huge effort in identifying the general elements involved in membrane curvature, the physical-chemical basis of curvature induction is still poorly understood. In this work, we fill this gap by engineering a minimal curvature-inducing system. Due to its exclusive nanoengineering properties, DNA origami technology will be utilized to build minimal curvature-inducing scaffoldings. This state-of-the-art technology enables the folding of long strands of DNA into nano-objects with defined shapes by using sequence-specific short DNA staples. For instance, our group recently constructed membrane-interacting rod-like DNA origami structures, which were functionalized with hydrophobic anchors and fluorescently labeled at defined positions [1]. Here, synthetic nanostructures will be designed in order to have a) defined customized shapes and b) specific membrane binding elements. Hybrid origami scaffolds with specific functional membrane-attachment groups bound at defined positions on the scaffolds will be produced. The interaction of those hybrid scaffolds with lipid membrane model systems will be studied and their capability of inducing membrane curvature evaluated. Fluorescence microscopy and atomic force microscopy methods will be used in order to retrieve extent, localization and forces involved in the interactions. More precisely, the role of the scaffolding shapes, membrane-attachment moieties, oligomerization and conformational changes will be assessed. At the end, this quantitative characterization of minimal membrane-inducing scaffolds will help understand the role of cooperativity in membrane deformation and the rules that govern the induction of membrane curvature.[1] A. Czogalla, E. P. Petrov, D. J. Kauert, V. Uzunova, Y. Zhang, R. Seidel, and P. Schwille, Faraday Discuss. 161 (2013) 31.

Molecular Threading and Tunable Molecular Recognition on DNA Origami Nanostructures

The DNA origami technology holds great promise for the assembly of nanoscopic technological devices and studies of biochemical reactions at the single-molecule level. For these, it is essential to establish well controlled attachment of functional materials to predefined sites on the DNA origami nanostructures for reliable measurements and versatile applications. However, the two-sided nature of the origami scaffold has shown limitations in this regard. We hypothesized that holes of the commonly used two-dimensional DNA origami designs are large enough for the passage of single-stranded (ss)-DNA. Sufficiently long ssDNA initially located on one side of the origami should thus be able to "thread" to the other side through the holes in the origami sheet. By using an origami sheet attached with patterned biotinylated ssDNA spacers and monitoring streptavidin binding with atomic force microscopic (AFM) imaging, we provide unambiguous evidence that the biotin ligands positioned on one side have indeed threaded through to the other side. Our finding reveals a previously overlooked critical design feature that should provide new interpretations to previous experiments and new opportunities for the construction of origami structures with new functional capabilities.

DNA origami technology for biomaterials applications.

DNA origami is an emerging technology for designing and constructing defined multidimensional nanostructures. This technology is now expanding to materials science. This article introduces the basics of DNA origami, the design of various two-dimensional and three-dimensional DNA origami structures, and the programmed assembly of origami structures. DNA origami has unique properties, such as an addressable surface, which enables selective functionalization with biomolecules and nanomaterials. The origami can also be combined with top-down nanotechnology, such as placement on a fabricated substrate. The technology is also applied to single-molecule imaging and analysis systems constructed on designed DNA origami structures. Furthermore, DNA mechanical nanodevices working on DNA origami have been realized, and cell-oriented applications are now in progress. DNA origami technology has practical potential in various research fields.

ChemInform Abstract: DNA Origami: The Art of Folding DNA.

AbstractReview: 61 refs.

DNA Origami: The Art of Folding DNA

The advent of DNA origami technology greatly simplified the design and construction of nanometer-sized DNA objects. The self-assembly of a DNA-origami structure is a straightforward process in which a long single-stranded scaffold (often from the phage M13mp18) is folded into basically any desired shape with the help of a multitude of short helper strands. This approach enables the ready generation of objects with an addressable surface area of a few thousand nm(2) and with a single "pixel" resolution of about 6 nm. The process is rapid, puts low demands on experimental conditions, and delivers target products in high yields. These features make DNA origami the method of choice in structural DNA nanotechnology when two- and three-dimensional objects are desired. This Minireview summarizes recent advances in the design of DNA origami nanostructures, which open the door to numerous exciting applications.

Organizing DNA Origami Tiles into Larger Structures Using Preformed Scaffold Frames

Structural DNA nanotechnology utilizes DNA molecules as programmable information-coding polymers to create higher order structures at the nanometer scale. An important milestone in structural DNA nanotechnology was the development of scaffolded DNA origami in which a long single-stranded viral genome (scaffold strand) is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides (staple strands). The achievable dimensions of the DNA origami tile units are currently limited by the length of the scaffold strand. Here we demonstrate a strategy referred to as "superorigami" or "origami of origami" to scale up DNA origami technology. First, this method uses a collection of bridge strands to prefold a single-stranded DNA scaffold into a loose framework. Subsequently, preformed individual DNA origami tiles are directed onto the loose framework so that each origami tile serves as a large staple. Using this strategy, we demonstrate the ability to organize DNA origami nanostructures into larger spatially addressable architectures.

Analogic China map constructed by DNA

In this research, a nanoscale DNA structure of analogic China map is created. The nanostructure of roughly 150 nm in diameter with a spatial resolution of 6 nm is purely constructed by folding DNA. The picture observed by atomic force microscopy (AFM) is almost identical with the designed shape. The DNA origami technology invented by Rothemund in 2006 is employed in the construction of this shape, which has proved the capability of constructing almost any complicated shape enabled by DNA origami, and provides new bottom-up method for constructing nanostructures.